Discover our collection of 4 research tools and applications for virology.
Found 4 of 4 tools
Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Some QUIck Reconstruction to Resolve Evolutionary Links Squirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation.